Inhibition of genetic expression by the direct interaction of probe molecules with specifically targeted sequences of DNA or mRNA is a fundamental approach to the chemotherapeutic treatment of viral and oncogenic diseases. Selective inhibition of gene expression using antisense oligonucleotides exploits the base-pairing capability of DNA or mRNA to escort the antisense probe to a targeted sequence of nucleic acids, thereby making this approach to chemotherapy exceptionally specific. The studies described in this proposal use a "modified nucleic acid" strategy for template-directed covalent alkylation of DNA. This process will be achieved by the chemical synthesis of suitably functionalized modified nucleic acids, the incorporation of these bases into oligonucleotides, and the post-synthetic attachment of an electrophilic tether. Upon duplex formation with a complementary oligonucleotide strand, a covalent cross-link will be formed between the probe oligonucleotide and a nucleophilic group on the complementary strand. The consequence of this process will be the creation of an indelible lesion that will irreversibly mask the genetic information contained within the targeted oligonucleotide molecule. Such covalent oligonucleotide probes could provide the basis for a valuable new class of highly specific pharmacological agents for antisense inhibition of oncogenic, genetic, and viral diseases.